Temporal changes of genetic structure and diversity in a marine diatom genus discovered via metabarcoding

Abstract

Diatoms’ bloom dynamics, with seasonal cycling of waxes and wanes of cell abundance, imply frequent bottleneck and expansion events that can leave signatures in the genetic structure and diversity of populations. We explored changes in genetic diversity and structure within multiple species of the planktonic marine diatom genus Pseudo‐nitzschia living in sympatry in the Gulf of Naples (Tyrrhenian Sea, Italy) over 48 sampling dates (from 2011 to 2013) by means of metabarcode data. The genus Pseudo‐nitzschia includes complexes of cryptic species along with morphologically distinguishable ones. We assessed the resolution power of the hypervariable V4 region of the 18S rDNA in delimiting species using different algorithms and a set of reference sequences. We measured intra‐specific genetic diversity and differentiation among species over three annual cycles. Between‐species divergence was higher in the P. pseudodelicatissima complex, while signs of incomplete lineage sorting and/or introgression were detected in the P. delicatissima complex. Most of the species showed significant population differentiation over time, due to changes in haplotypic composition over the three years. Some haplotypes were lost and new ones appeared, with high polymorphism in species of the P. delicatissima complex. We hypothesize that the observed temporal changes in genetic structure result from frequent founder events linked to a population dynamic characterized by cyclical alternation of clonal expansions and bottlenecks and discuss possible factors affecting the microevolutionary pathways in these planktonic diatoms.

Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected genera

“…Lastly, we discuss the potential of rbcL metabarcoding to draw meaningful conclusions about population structure and microevolution. We focused on two widely studied groups, and in the case of Pseudo-nitzschia galaxiae , one species for which speciation hypotheses exist ( Ruggiero et al, 2015 , 2022 ; Turk Dermastia et al, 2022 ). When using metabarcoding as a population genetics tool, caution must be exercised with sequencing technology and ASV calling algorithms, which are not error-prone and therefore can artificially inflate haplotype composition ( Nearing et al, 2018 ; Turon et al, 2020 ).…”

Phenological segregation suggests speciation by time in the planktonic diatom Pseudo‐nitzschia allochrona sp. nov.

“…Since its first record in 2004 (as “ Pseudo‐nitzschia new genotype”) in a clone library‐based DNA‐metabarcoding study of the 28S rDNA fragment (McDonald et al, 2007 ), P. allochrona has always been the only species of the group found in summer–autumn, never showing up among the more than 187 strains of the P. delicatissima ‐complex retrieved in winter–spring in the area over more than 10 years, all invariably identified as P. delicatissima , P. arenysensis , or P. dolorosa . Temporal segregation is also confirmed by an annual overview based on 28S rDNA clone library, in which P. allochrona (as P. delicatissima IV) was responsible for the late summer‐early autumn blooms of 2009 and 2010 (Ruggiero et al, 2015 ), while a three‐year HTS study based on 17,763 environmental 18S rDNA‐V4 barcodes has again shown P. allochrona to be abundant in summer in 2011 and 2013 (Ruggiero et al, 2022 ). In all the three above‐mentioned metabarcoding studies, P. arenysensis/P.…”

“…was responsible for the late summer-early autumn blooms of 2009 and 2010 (Ruggiero et al, 2015), while a three-year HTS study based on 17,763 environmental 18S rDNA-V4 barcodes has again shown P. allochrona to be abundant in summer in 2011 and 2013 (Ruggiero et al, 2022). In all the three above-mentioned metabarcoding studies, P. arenysensis/P.…”

“…Another species in the P. delicatissima ‐complex, P. dolorosa , also found in the GoN, is also not distinguishable from P. allochrona in LM but has a lower density of interstriae, fibulae and poroids, and may have one or two rows of poroids (Lim et al, 2012 ; Lundholm et al, 2006 ). Among the other P. delicatissima ‐like species, two were occasionally found in the Gulf of Naples by isolation or metabarcoding (Ruggiero et al, 2022 ). P. micropora is distinct from P. allochrona because it lacks a central nodule in the larger interspace between the two central fibulae (Ajani et al, 2013 ; Priisholm et al, 2002 ), while P. decipiens has a higher density of interstriae (41–47 in 10 μm) and band striae (48–55 in 10 μm; Lundholm et al, 2006 ; Teng et al, 2015 ).…”

“…Peaks of P. arenysensis in some years followed and in other years preceded those of P. delicatissima , which actually co‐occurred with P. allochrona in late June‐early July of 2013. Interestingly, detailed molecular investigations on individual Pseudo‐nitzschia haplotypes from the 3‐year HTS dataset revealed an intragenomic P. allochrona variant intermediate between the prevalent P. allochrona and P. arenysensis haplotypes, as well a small number of P. allochrona haplotypes in early winter (Ruggiero et al, 2022 ).…”